After Apollomon absorbed Axemon, his even darker side of his dark side, Apollomon Whispered Darkness Mode was born. Apollomon reappeared along with the other Death Generals as soulless Digimon, and combined together to form the ultimate Death General, GrandGeneramon.
Apollomon was mistakenly and forcefully chosen as Death General and because of his suspicions, Bagramon placed a program into him called 'Whispered', thereby modifying his data. Apollomon punished or gave bad treatment to his people to turn their sadness into negative energy but keeping them alive as well as making wounds on his left arm covered with bandages. Whispered, however, reported everything to Bagramon and AxeKnightmon and deleted every Digimon that failed him.
When Mikey, Nene and Christopher arrive at Bright Land, he sends Marsmon and Sethmon at them to test their power to see if they are the ones he was waiting for. After they defeat them, he allows them to climb up Apollonia Tower and meet him. He tries to convince them to rebel with him against Bagramon but no avail as Nene and Christopher do not want to believe him. After the Whispered program takes over Apollomon's body and deletes Marsmon, Apollomon shields Taiki from MetalGreymon's attack with his wounded arm making everybody believe him. However, as soon as that happens, Ewan Amano breaks into the tower with the portal Whispered opens. Then Whispered takes full control of Apollomon's body while revealing the truth behind Apollomon and others why he is a Death General. After the explanation, Apollomon tells Mikey to kill him. But before they could do anything, Whispered has Apollomon send the Fusion Fighters to Hell's Field.
When in Hell's Field, he fought alongside Ewan and AxeKnightmon. During the battle, Whispered forcibly DigiFused him with Axemon to form a Darkness Mode. After the Xros Heart United Army's victory against Yu on the Hell Field, Apollomon Whispered forced Laylamon to merged with Blastmon to become a monster that starts destroying Hell Field to keep the Xros Heart United Army from leaving. But in the end, Laylamon was finally destroyed when Beelzemon sacrificed himself to defeat her.
When Laylamon ends up starting to negate the effects of the Hell's Field, Apollomon Whispered manages to get out. Once his enemies escaped as well, Mikey proceeded to go fight Apollomon Whispered Mode. Upon the advice of Apollomon trying to fight Whispered's control, Mikey hesitantly has Shoutmon X7 destroy both Apollomon and Whispered.
AxeKnightmon later uses the Darkness Stone to revive Apollomon without his DigiCore. His body was used as a component for GrandGeneramon. When Mikey ends up in Prison Land to rescue the DigiCores of Shoutmon, Ballistamon, and Dorulumon, Whispered and the other Dark Generals encountered them. Olegmon betrayed the other Dark Generals, and he and Shoutmon X3 fought back Whispered. Whispered asks the Dark Generals to help him, but they refused. Whispered then heard Apollomon's voice, shocking him. Whispered forced his good side out of his body. Whispered attempts to erase his alter-ego, but Apollomon defeats and erases his dark side of himself for good.
- Whispering Arrow: Continuously fires dark arrows from the shining jewels on his hands.
- Sun of Lamentation: Gathers solar energy into an ever-expanding dark sun that incinerates all that it touches.